[2024-01-24 11:22:49,302] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:22:49,303] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:22:49,303] [INFO] DQC Reference Directory: /var/lib/cwl/stg5428b0e6-8403-40b4-a78a-c431eca65622/dqc_reference
[2024-01-24 11:22:50,484] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:22:50,484] [INFO] Task started: Prodigal
[2024-01-24 11:22:50,485] [INFO] Running command: gunzip -c /var/lib/cwl/stgc9a350e6-4e7d-4b48-bcbe-d076c03db578/GCF_016746095.1_ASM1674609v1_genomic.fna.gz | prodigal -d GCF_016746095.1_ASM1674609v1_genomic.fna/cds.fna -a GCF_016746095.1_ASM1674609v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:23:12,562] [INFO] Task succeeded: Prodigal
[2024-01-24 11:23:12,562] [INFO] Task started: HMMsearch
[2024-01-24 11:23:12,562] [INFO] Running command: hmmsearch --tblout GCF_016746095.1_ASM1674609v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5428b0e6-8403-40b4-a78a-c431eca65622/dqc_reference/reference_markers.hmm GCF_016746095.1_ASM1674609v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:23:12,878] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:23:12,880] [INFO] Found 6/6 markers.
[2024-01-24 11:23:12,925] [INFO] Query marker FASTA was written to GCF_016746095.1_ASM1674609v1_genomic.fna/markers.fasta
[2024-01-24 11:23:12,925] [INFO] Task started: Blastn
[2024-01-24 11:23:12,926] [INFO] Running command: blastn -query GCF_016746095.1_ASM1674609v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5428b0e6-8403-40b4-a78a-c431eca65622/dqc_reference/reference_markers.fasta -out GCF_016746095.1_ASM1674609v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:23:13,542] [INFO] Task succeeded: Blastn
[2024-01-24 11:23:13,545] [INFO] Selected 17 target genomes.
[2024-01-24 11:23:13,545] [INFO] Target genome list was writen to GCF_016746095.1_ASM1674609v1_genomic.fna/target_genomes.txt
[2024-01-24 11:23:13,552] [INFO] Task started: fastANI
[2024-01-24 11:23:13,553] [INFO] Running command: fastANI --query /var/lib/cwl/stgc9a350e6-4e7d-4b48-bcbe-d076c03db578/GCF_016746095.1_ASM1674609v1_genomic.fna.gz --refList GCF_016746095.1_ASM1674609v1_genomic.fna/target_genomes.txt --output GCF_016746095.1_ASM1674609v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:23:28,225] [INFO] Task succeeded: fastANI
[2024-01-24 11:23:28,226] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5428b0e6-8403-40b4-a78a-c431eca65622/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:23:28,227] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5428b0e6-8403-40b4-a78a-c431eca65622/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:23:28,242] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:23:28,242] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:23:28,243] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Sphingobacterium faecale	strain=C459-1	GCA_016746095.1	2803775	2803775	type	True	100.0	1774	1777	95	conclusive
Sphingobacterium paucimobilis	strain=HER1398	GCA_000416985.1	1385985	1385985	type	True	89.5269	1099	1777	95	below_threshold
Sphingobacterium tabacisoli	strain=h337	GCA_017908035.1	2044855	2044855	type	True	86.0461	950	1777	95	below_threshold
Sphingobacterium yanglingense	strain=DSM 28353	GCA_004363245.1	1437280	1437280	type	True	83.1094	883	1777	95	below_threshold
Sphingobacterium nematocida	strain=DSM 24091	GCA_900168125.1	1513896	1513896	type	True	80.1125	591	1777	95	below_threshold
Sphingobacterium composti Yoo et al. 2007 non Ten et al. 2007	strain=DSM 18850	GCA_008124885.1	415956	415956	type	True	78.9564	105	1777	95	below_threshold
Sphingobacterium rhinopitheci	strain=WQ 047	GCA_022627575.1	2781960	2781960	type	True	78.3019	190	1777	95	below_threshold
Sphingobacterium bovisgrunnientis	strain=KCTC 52685	GCA_009829085.1	1874697	1874697	type	True	78.2524	192	1777	95	below_threshold
Sphingobacterium soli	strain=CGMCC 1.15966	GCA_014644335.1	1914757	1914757	type	True	77.7876	140	1777	95	below_threshold
Sphingobacterium prati	strain=arapr2	GCA_013167215.1	2737006	2737006	type	True	77.665	118	1777	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:23:28,244] [INFO] DFAST Taxonomy check result was written to GCF_016746095.1_ASM1674609v1_genomic.fna/tc_result.tsv
[2024-01-24 11:23:28,245] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:23:28,245] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:23:28,245] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5428b0e6-8403-40b4-a78a-c431eca65622/dqc_reference/checkm_data
[2024-01-24 11:23:28,247] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:23:28,296] [INFO] Task started: CheckM
[2024-01-24 11:23:28,296] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016746095.1_ASM1674609v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016746095.1_ASM1674609v1_genomic.fna/checkm_input GCF_016746095.1_ASM1674609v1_genomic.fna/checkm_result
[2024-01-24 11:24:30,188] [INFO] Task succeeded: CheckM
[2024-01-24 11:24:30,190] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:24:30,212] [INFO] ===== Completeness check finished =====
[2024-01-24 11:24:30,212] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:24:30,213] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016746095.1_ASM1674609v1_genomic.fna/markers.fasta)
[2024-01-24 11:24:30,213] [INFO] Task started: Blastn
[2024-01-24 11:24:30,213] [INFO] Running command: blastn -query GCF_016746095.1_ASM1674609v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5428b0e6-8403-40b4-a78a-c431eca65622/dqc_reference/reference_markers_gtdb.fasta -out GCF_016746095.1_ASM1674609v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:24:30,978] [INFO] Task succeeded: Blastn
[2024-01-24 11:24:30,987] [INFO] Selected 12 target genomes.
[2024-01-24 11:24:30,988] [INFO] Target genome list was writen to GCF_016746095.1_ASM1674609v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:24:31,001] [INFO] Task started: fastANI
[2024-01-24 11:24:31,002] [INFO] Running command: fastANI --query /var/lib/cwl/stgc9a350e6-4e7d-4b48-bcbe-d076c03db578/GCF_016746095.1_ASM1674609v1_genomic.fna.gz --refList GCF_016746095.1_ASM1674609v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016746095.1_ASM1674609v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:24:41,785] [INFO] Task succeeded: fastANI
[2024-01-24 11:24:41,794] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:24:41,794] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_016746095.1	s__Sphingobacterium sp016746095	100.0	1774	1777	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000416985.1	s__Sphingobacterium paucimobilis	89.5423	1098	1777	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017908035.1	s__Sphingobacterium tabacisoli	86.044	950	1777	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004363245.1	s__Sphingobacterium yanglingense	83.095	884	1777	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011007365.1	s__Sphingobacterium sp011007365	81.0134	563	1777	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	99.58	99.33	0.95	0.93	4	-
GCF_900168125.1	s__Sphingobacterium nematocida	80.1225	589	1777	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008124885.1	s__Sphingobacterium composti_A	78.9546	105	1777	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011043525.1	s__Sphingobacterium sp011043525	77.6874	114	1777	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:24:41,799] [INFO] GTDB search result was written to GCF_016746095.1_ASM1674609v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:24:41,799] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:24:41,803] [INFO] DFAST_QC result json was written to GCF_016746095.1_ASM1674609v1_genomic.fna/dqc_result.json
[2024-01-24 11:24:41,803] [INFO] DFAST_QC completed!
[2024-01-24 11:24:41,803] [INFO] Total running time: 0h1m53s